BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008708.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,948,619 number of mapped reads = 1,394,275 (71.55%) number of supplementary alignments = 5,192 (0.27%) number of secondary alignments = 0 number of mapped bases = 92,804,574 bp number of sequenced bases = 92,758,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,834 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5687 >>>>>>> ACTG content number of A's = 28,482,239 bp (30.71%) number of C's = 15,724,608 bp (16.95%) number of T's = 27,812,979 bp (29.98%) number of G's = 20,717,314 bp (22.33%) number of N's = 21,336 bp (0.02%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 882,637 number of insertions = 7,036 mapped reads with insertion percentage = 0.5% number of deletions = 29,461 mapped reads with deletion percentage = 2.09% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.03X std coverageData = 0.2352X There is a 2.71% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7576421 0.030396798891024628 0.3214579491805005 chr2 243199373 8615750 0.03542669495286898 0.2889369688920947 chr3 198022430 7763393 0.03920461434596071 0.21978341427374562 chr4 191154276 5209607 0.027253415979038836 0.18224670598905304 chr5 180915260 4855315 0.02683750945055713 0.179375856048904 chr6 171115067 5210342 0.030449346696045182 0.20705514148744109 chr7 159138663 5010548 0.031485422244624486 0.29712760704558894 chr8 146364022 7266180 0.04964457727186535 0.3339960985370273 chr9 141213431 3148467 0.022295804143445817 0.202123518469592 chr10 135534747 5096603 0.037603663361691304 0.24805346506103632 chr11 135006516 4008327 0.029689878079662467 0.2274779745224219 chr12 133851895 4148337 0.030991993053217513 0.19533025947951563 chr13 115169878 2803861 0.02434543692058092 0.1740835418345417 chr14 107349540 2859482 0.026637114607104977 0.1841830754215685 chr15 102531392 2224955 0.021700232061610945 0.16452284403162862 chr16 90354753 2141100 0.023696595130972248 0.1804952328973593 chr17 81195210 2255233 0.027775443896259397 0.20015620496188888 chr18 78077248 2020101 0.02587310710541437 0.33496787056674754 chr19 59128983 1325587 0.02241856586642121 0.20477847497560497 chr20 63025520 1989068 0.03155972374365178 0.196171739064528 chr21 48129895 967321 0.02009813235619982 0.16030348167216807 chr22 51304566 898671 0.017516394154859432 0.14402126760557576 chrMT 16571 21840 1.3179651197875808 1.655486893112941 chrX 155270560 5196187 0.033465371671229885 0.2110315484449965 chrY 59373566 191878 0.0032317075245236236 0.07447084022211287